On my machine, I replaced the Control modifier key for the Spotlight commands with Command. This is simple, since it changes it for all applications, and doesn't usually conflict with anything else.

System Preferences > Keyboard > Keyboard Shortcuts > Spotlight

Alternatively, you could add an additional modifier, e.g., ⌃-⌥-space. Or even change it altogether. I've used ⌃-⌘-F in the past, for example; though that's now the default key for Full Screen on Lion.

The default Spotlight keys are the main conflict with Terminal. I don't think there are other default shortcut keys that are a problem (because they either don't use Control, or if they do they usually use other modifiers or keys that don't conflict with how Terminal handles keyboard input).